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| Preface to the First Edition | |
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| Preface to the Second Edition | |
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| Preface to the Third Edition | |
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| Acknowledgments | |
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| Virology and Viral Disease | |
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| Introduction � the Impact of Viruses on Our View of Life 2 | |
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| The Science Of Virology | |
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| The Effect of Virus Infections on the Host Organism and Populations � Viral Pathogenesis, Virulence, and Epidemiology | |
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| The Interaction Between Viruses and Their Hosts | |
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| The History of Virology | |
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| Examples of the Impact of Viral Disease on Human History | |
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| Examples of the Evolutionary Impact of the Virus�Host Interaction | |
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| The Origin of Viruses | |
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| Viruses Have a Constructive as Well as Destructive Impact on Society | |
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| Viruses are Not the Smallest Self-replicating Pathogens | |
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| An Outline of Virus Replication and Viral Pathogenesis | |
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| Virus Replication | |
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| Stages of Virus Replication in the Cell | |
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| Pathogenesis Of Viral Infection | |
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| Stages of Virus-induced Pathology | |
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| Virus Disease in Populations and Individual Animals | |
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| The Nature Of Virus Reservoirs | |
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| Some Viruses with Human Reservoirs | |
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| Some Viruses with Vertebrate Reservoirs | |
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| Viruses In Populations | |
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| Viral Epidemiology in Small and Large Populations | |
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| Factors Affecting the Control of Viral Disease in Populations | |
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| Animal Models To Study Viral Pathogenesis | |
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| A Mouse Model for Studying Poxvirus Infection and Spread | |
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| Rabies: Where is the Virus During its Long Incubation Period? | |
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| Herpes Simplex Virus Latency | |
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| Patterns of Some Viral Diseases of Humans | |
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| The Stable Association of Viruses with their Natural Host Places Specific Constraints on the Nature of Viral Disease and Mode of Persistence | |
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| Classification of Human Disease-Causing Viruses According to Virus�Host Dynamics | |
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| Patterns Of Specific Viral Diseases Of Humans | |
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| Acute Infections Followed by Virus Clearing | |
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| Infection of an �Accidental� Target Tissue Leading to Permanent Damage Despite Efficient Clearing | |
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| Persistent Viral Infections | |
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| Viral and Subviral Diseases with Long Incubation Periods | |
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| Some Viral Infections Targeting Specific Organ Systems | |
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| Viral Infections of Nerve Tissue | |
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| Examples of Viral Encephalitis with Grave Prognosis | |
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| Viral Encephalitis with Favorable Prognosis for Recovery | |
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| Viral Infections of the Liver (Viral Hepatitis | |
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| Problems For Part I | |
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| Additional Reading For Part I | |
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| Basic Properties of Viruses and Virus�Cell Interaction | |
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| Virus Structure and Classification | |
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| The Features Of A Virus | |
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| Viral Genomes | |
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| Viral Capsids | |
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| Viral Envelopes | |
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| Classification Schemes | |
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| The Baltimore Scheme of Virus Classification | |
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| Disease-based Classification Schemes for Viruses | |
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| The Virosphere | |
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| The Beginning and End of the Virus Replication Cycle | |
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| Outline of the Virus Replication Cycle | |
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| Viral Entry | |
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| Mechanisms of Entry of Nonenveloped Viruses | |
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| Entry of Enveloped Viruses | |
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| Entry of Virus into Plant Cells | |
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| Injection of Bacteriophage DNA into Escherichia coli | |
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| Nonspecific Methods of Introducing Viral Genomes into Cells | |
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| Late Events In Viral Infection: Capsid Assembly And Virion Release | |
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| Assembly of Helical Capsids | |
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| Assembly of Icosahedral Capsids | |
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| Generation of the Virion Envelope and Egress of the Enveloped Virion | |
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| Host Immune Response to Viral Infection � The Nature of the Vertebrate Immune Response | |
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| The Innate Immune Response � Early Defense Against Pathogens | |
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| Toll-like Receptors | |
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| Defensins | |
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| The Adaptive Immune Response And The Lymphatic System | |
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| Two Pathways of Helper T Response: the Fork in the Road | |
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| The Immunological Structure of a Protein | |
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| Role of the Antigen-presenting Cell in Initiation of the Immune Response | |
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| Control And Dysfunction Of Immunity | |
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| Specific Viral Responses to Host Immunity | |
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| Consequences of Immune Suppression to Virus Infections | |
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| Measurement Of The Immune Reaction | |
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| Measurement of Cell-mediated (T-cell) Immunity | |
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| Measurement of Antiviral Antibody | |
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| Strategies to Protect Against and Combat Viral Infection | |
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| Vaccination � Induction Of Immunity To Prevent Virus Infection | |
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| Antiviral Vaccines | |
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| Smallpox and the History of Vaccination | |
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| How a Vaccine is Produced | |
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| Problems with Vaccine Production and Use | |
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| Eukaryotic Cell-Based Defenses Against Virus Replication | |
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| Interferon | |
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| Other Cellular Defenses against Viral Infection | |
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| Antiviral Drugs | |
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| Targeting Antiviral Drugs to Specific Features of the Virus Replication Cycle | |
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| Other Approaches | |
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| Bacterial Antiviral Systems � Restriction Endonucleases | |
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| Problems For Part II | |
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| Additional Reading For Part II | |
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| Working with Virus | |
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| Visualization and Enumeration of Virus Particles | |
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| Using the Electron Microscope to Study and Count Viruses | |
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| Atomic Force Microscopy � A Rapid and Sensitive Method for Visualization of Viruses and Infected Cells, Potentially in Real Time | |
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| Indirect Methods for �Counting� Virus Particles | |
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| Replicating and Measuring Biological Activity of Viruses | |
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| Cell Culture Techniques | |
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| Culture of Animal and Human Cells | |
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| The Outcome Of Virus Infection In Cells | |
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| Fate of the Virus | |
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| Fate of the Cell Following Virus Infection | |
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| Measurement Of The Biological Activity Of Viruses | |
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| Quantitative Measure of Infectious Centers | |
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| Use of Virus Titers to Quantitatively Control Infection Conditions | |
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| Dilution Endpoint Methods | |
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| Physical and Chemical Manipulation of the Structural Components of Viruses | |
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| Viral Structural Proteins | |
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| Isolation of Structural Proteins of the Virus | |
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| Size Fractionation of Viral Structural Proteins | |
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| Characterizing Viral Genomes | |
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| Sequence Analysis of Viral Genomes | |
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| Measuring the Size of Viral Genomes | |
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| The Polymerase Chain Reaction � Detection and Characterization of Extremely Small Quantities of Viral Genomes or Transcripts | |
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| Characterization of Viral Products Expressed in the Infected Cell | |
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| Characterization Of Viral Proteins In The Infected Cell | |
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| Pulse Labeling of Viral Proteins at Different Times Following Infection | |
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| Use of Immune Reagents for Study of Viral Proteins | |
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| Detecting And Characterizing Viral Nucleic Acids In Infected Cells | |
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| Characterization of Viral mRNA Expressed During Infection | |
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| Use Of Microarray Technology For Getting A Complete Picture Of The Events Occurring In The Infected Cell | |
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| Viruses Use Cellular Processes to Express Their Genetic Information | |
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| Prokaryotic DNA Replication is an Accurate Enzymatic Model for the Process Generally | |
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| Expression of mRNA | |
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| Prokaryotic Transcription | |
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| Eukaryotic Transcription | |
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| The Mechanism of Protein Synthesis | |
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| Problems For Part III | |
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| Additional Reading For Part III | |
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| Replication Patterns of Specific Viruses | |
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| Replication of Positive-sense RNA Viruses | |
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| RNA Viruses � General Considerations | |
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| A General Picture of RNA-Directed RNA Replication | |
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| Replication Of Positive-Sense Rna Viruses Whose Genomes Are Translated As The First Step In Gene Expression | |
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| Positive-Sense Rna Viruses Encoding A Single Large Open Reading Frame | |
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| Picornavirus Replication | |
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| Flavivirus Replication | |
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| Positive-sense RNA Viruses Encoding More than One Translational Reading Frame | |
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| Two Viral mRNAs are Produced in Different Amounts During Togavirus Infections | |
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| A Somewhat More Complex Scenario of Multiple Translational Reading Frames and Subgenomic mRNA Expression: Coronavirus Replication | |
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| Replication Of Plant Viruses With Rna Genomes | |
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| Viruses with One Genome Segment | |
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| Viruses with Two Genome Segments | |
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| Viruses with Three Genome Segments | |
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| Replication Of Bacteriophage With Rna Genomes | |
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| Regulated Translation of Bacteriophage mRNA | |
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| Replication Strategies of RNA Viruses Requiring RNA-directed mRNA Transcription as the First Step in Viral Gene Expression | |
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| Paramyxoviruses | |
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| Filoviruses and their Pathogenesis | |
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| Bornaviruses | |
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| Influenza Viruses � Negative-Sense Rna Viruses With A Multipartite Genome | |
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| Involvement of the Nucleus in Flu Virus Replication | |
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| Generation of New Flu Nucleocapsids and Maturation of the Virus | |
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| Influenza A Epidemics | |
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| Other Negative-Sense Rna Viruses With Multipartite Genomes | |
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| Bunyaviruses | |
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| Arenaviruses | |
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| Viruses With Double-Stranded Rna Genomes | |
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| Reovirus Structure | |
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| Reovirus Replication Cycle | |
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| Pathogenesis | |
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| Subviral Pathogens | |
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| Hepatitis Delta Virus | |
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| Viroids | |
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| Prions | |
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| Replication Strategies of Small and Medium-sized DNA Viruses | |
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| DNA Viruses Express Genetic Information and Replicate Their Genomes in Similar, Yet Distinct, Ways | |
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| Papovavirus Replication | |
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| Replication of SV40 Virus � The Model Polyomavirus | |
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| Replication of Papillomaviruses | |
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| Replication of Adenoviruses | |
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| Physical Properties of Adenovirus | |
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| The Adenovirus Replication Cycle | |
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| Replication of Some Single-stranded DNA Viruses | |
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| Replication of Parvoviruses | |
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| DNA Viruses Infecting Vascular Plants | |
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| Single-stranded DNA Bacteriophage X174 Packages its Genes Very Compactly | |
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| Replication of Some Nuclear-replicating Eukaryotic DNA Viruses with Large Genomes | |
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| Herpesvirus Replication And Latency | |
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| The Herpesviruses as A Group | |
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| The Replication of the Prototypical Alpha-Herpesvirus � HSV | |
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| HSV Latency and LAT | |
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| EBV Latent Infection of Lymphocytes, A Different Set of Problems and Answers | |
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| Pathology of Herpesvirus Infections | |
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| Baculovirus, An Insect Virus With Important Practical Uses In Molecular Biology | |
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| Virion Structure | |
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| Viral Gene Expression and Genome Replication | |
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| Pathogenesis | |
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| Importance of Baculoviruses in Biotechnology | |
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| Replication of Cytoplasmic DNA Viruses and �Large� Bacteriophages | |
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| Poxviruses � Dna Viruses That Replicate In The Cytoplasm Of Eukaryotic Cells | |
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| The Pox Virion is Complex and Contains Virus-coded Transcription Enzymes | |
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| The Poxvirus Replication Cycle | |
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| Pathogenesis and History of Poxvirus Infections | |
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| Is Smallpox Virus A Potential Biological Terror Weapon? | |
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| Replication Of �Large� Dna-Containing Bacteriophages | |
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| Components of Large DNA-containing Phage Virions | |
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| Replication of Phage T7 | |
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| T4 Bacteriophage: the Basic Model for All DNA Viruses | |
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| Replication of Phage : a �Simple� Model for Latency and Reactivation | |
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| A Group Of Algal Viruses Shares Features Of Its Genome Structure With Poxviruses And Bacteriophages | |
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| Retroviruses: Converting RNA to DNA | |
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| Retrovirus Families And Their Strategies Of Replication | |
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| The Molecular Biology of Retrovirus | |
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| Replication of Retroviruses: An Outline of the Replication Process | |
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| Viral Gene Expression, Assembly, and Maturation | |
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| Mechanisms Of Retrovirus Transformation | |
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| Transformation through the Action of A Viral Oncogene � A Subverted Cellular Growth Control Gene | |
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| Oncornavirus Alteration of Normal Cellular Transcriptional Control of Growth Regulation | |
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| Oncornavirus Transformation by Growth Stimulation of Neighboring Cells | |
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| Cellular Genetic Elements Related To Retroviruses | |
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| Retrotransposons | |
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| The Relationship Between Transposable Elements and Viruses | |
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| Human Immunodeficiency Virus Type 1 (HIV-1) and Related Lentiviruses | |
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| HIV-1 and Related Lentiviruses | |
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| The Origin of HIV-1 and AIDS | |
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| HIV-1 and Lentiviral Replication | |
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| Destruction of the Immune System by HIV-1 | |
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| Hepadnaviruses: Variations on the Retrovirus Theme | |
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| The Virion and the Viral Genome | |
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| The Viral Replication Cycle | |
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| The Pathogenesis of Hepatitis B Virus | |
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| A Plant �Hepadnavirus�: Cauliflower Mosaic Virus | |
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| The Evolutionary Origin of Hepadnaviruses | |
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| Problems For Part IV | |
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| Additional Reading For Part IV | |
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| Viruses: New Approaches and New Problems | |
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| The Molecular Genetics of Viruses | |
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| Mutations in Genes and Resulting Changes to Proteins | |
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| Analysis of Mutations | |
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| Isolation of Mutants | |
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| A Tool Kit For Molecular Virologists | |
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| Viral Genomes | |
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| Locating Sites of Restriction Endonuclease Cleavage On the Viral Genome � Restriction Mapping | |
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| Cloning Vectors | |
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| Directed Mutagenesis of Viral Genes | |
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| Generation of Recombinant Viruses | |
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| Molecular Pathogenesis | |
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| An Introduction To The Study Of Viral Pathogenesis | |
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| Animal Models | |
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| Choosing a model: Natural Host vs. Surrogate Models | |
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| Development of New Models: Transgenic Animals | |
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| Hybrid Models: the SCID-hu Mouse | |
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| Considerations Regarding the Humane Use of Animals | |
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| Methods For The Study Of Pathogenesis | |
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| Assays of Virulence | |
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| Analysis of Viral Spread within the Host | |
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| Resolving the Infection to the Level of Single Cells | |
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| Characterization Of The Host Response | |
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| Immunological Assays | |
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| Use of Transgenic Mice to Dissect Critical Components of the Host Immune Response That Modulate the Viral Infection | |
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| Viral Bioinformatics and Beyond | |
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| Bioinformatics | |
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| Bioinformatics and Virology | |
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| Biological Databases | |
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| Primary Databases | |
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| Secondary Databases | |
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| Composite Databases | |
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| Other Databases | |
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| Biological Applications | |
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| Similarity Searching Tools | |
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| Protein Functional Analysis | |
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| Sequence Analysis | |
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| Structural Modeling | |
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| Structural Analysis | |
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| Systems Biology And Viruses | |
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| Viral Internet Resources | |
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| Viruses and the Future � Promises and Problems | |
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| Clouds on the Horizon � Emerging Disease | |
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| What are the Prospects of Using Medical Technology to Eliminate Specific Viral and Other Infectious Diseases? | |
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| Silver Linings � Viruses as Therapeutic Agents | |
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| Why Study Virology? | |
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| Problems For Part V | |
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| Additional Reading For Part V | |
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| Appendix: Resource Center | |
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| Books of Historical and Basic Value | |
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| Books on Virology | |
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| Molecular Biology and Biochemistry Texts | |
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| Detailed Sources | |
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| Sources for Experimental Protocols | |
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| The Internet | |
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| Technical Glossary | |
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| Index | |